Publications Archives

J. E. Mastronunzio, Y. Huang, and D. R. Benson. 2009. Diminished Exoproteome of Frankia spp. in Culture and Symbiosis. Appl. Environ. Microbiol. 75: 6721-6728.

Williamson A*, Wickliffe KE*, Mellone BG, Song L, Karpen GH, Rape M. Identification of a physiological E2 module for the human anaphase-promoting complex. PNAS epub ahead of print.

Kikuchi, Y. L. Bomar and J. Graf. (2009) Stratified bacterial community in the bladder of the medicinal leech, Hirudo verbana. Environ. Microbiol. 11:2758-2770. Cover article

Pores-Fernando AT, Zweifach A. Calcium influx and signaling in cytotoxic T-lymphocyte lytic granule exocytosis. Immunol Rev. 2009 Sep;231(1):160-73. PMID: 19592494

Pores-Fernando AT, Ranaghan MY, Zweifach A. No specific subcellular localization of protein kinase C is required for cytotoxic T cell granule exocytosis. J Biol Chem. 2009 Sep 11;284(37):25107-15. Epub 2009 Jul 10. PMID: 19754896

Bickhart DM, Gogarten JP, Lapierre P, Tisa LS, Normand P, Benson DR (2009) Insertion sequence content reflects genome plasticity in strains of the root nodule actinobacterium Frankia. BMC Genomics. 2009 Oct 12;10(1):468

Bapteste E, O'Malley MA, Beiko RG, Ereshefsky M, Gogarten JP, Franklin-Hall L, Lapointe FJ, Dupre J, Dagan T, Boucher Y, Martin W (2009) Prokaryotic evolution and the tree of life are two different things. Biol Direct. 2009 Sep 29;4:34.

Olendzenski L, Gogarten JP (2009) Evolution of Genes and Organisms: The Tree/Web of Life in Light of Horizontal Gene Transfer. Annals of the New York Academy of Sciences 1178: 137-145 doi: 10.1111/j.1749-6632.2009.04998.x

Pores-Fernando, A. T., S. Gaur, M. J. Grybko, and A Zweifach. 2008. ERK activation is only one role of PKC in TCR-independent cytotoxic T cell granule exocytosis. Biochem Biophys Res Commun. 371: 630–634.

Tang, L., J. Franca-Koh, Y. Xiong, M. Y. Chen, Y. Long, R. M. Bickford, D. A. Knecht, P. A. Iglesias and P. N. Devreotes. 2008. tsunami, the Dictyostelium homolog of the Fused kinase, is required for polarization and chemotaxis. Genes Dev. 22:2278-2290.

Musial-Siwek, M., P. Y. Yeagle and D. A. Kendall. 2008. A small set of signal peptidase residues are perturbe by signal peptide binding. Chem. Biol. Drug Des. 72:140-146

Sallum, U. W., W. Ulysses and T. Chen. 2008. Inducible resistance of fish bacterial pathogens to the antimicrobial peptide cecropin B. Antimicrobial Agents Chemotherapy 53:3006-3012

Pimentel, T.A., Z. Yan, S. A. Jeffers, K. V. Holmes, R. S. Hodges, P. Burkhard. 2009. Peptide nanoparticles as novel immunogens: design and analysis of a prototypic severe acute respiratory syndrome vaccine. Chem. Biol. Drug Des. 73:53-61.

Zhaxybayeva O, Doolittle WF, Papke RT, Gogarten JP (2009) Intertwined Evolutionary Histories of Marine Synechococcus and Prochlorococcus marinus Genome Biology and Evolution: doi:10.1093/gbe/evp032

Longo, M.S., Carone, D.M., Marzelli, M., M.J. O’Neill, E. Green, NISC Sequencing Consortium, R.J. O’Neill. 2009. Distinct retroelement classes define evolutionary breakpoints demarcating sites of evolutionary novelty. BMC Genomics 10:334.

Brown J.D. and R.J. O’Neill. 2009. The Mysteries of Chromosome Evolution in Gibbons: Methylation Is a Prime Suspect. PLoS Genet 5(6): e1000501. doi:10.1371/journal.pgen.1000501.

O’Neill, R.J. and D.M. Carone. 2009. Chapter 4: The role of ncRNA in centromeres: lessons from marsupials. in: Centromere: structure and evolution ed: D. Ugarkovic, Springer Press. Pp77-101.

Gage, D. J., Herron, P. M., Arango-Pinedo, C., and Z. G. Cardon (2008). Live reports from the soil grain--the promise and challenge of microbiosensors. Functional Ecology 22:983.

C. Arango-Pinedo and D. J. Gage (2009) HPrK regulates succinate- mediated catabolite repression in the Gram negative symbiont Sinorhizobium meliloti. J. Bacteriol. 191:298-309

Zhang, N., Wang, Q. Ehlinger, A., Randles, L., Lary, J. W., Kang, Y., Haririnia, A., Storaska, A. J., Cole, J. L., Fushman, D., Walters, K. J. (2009) Structure of the S5a:K48-Linked Diubiquitin Complex and Its Interactions with Rpn13. Mol. Cell 35, 280-290.

Silver, A.C. and J. Graf. 2009. Prevalence of genes encoding type three secretion system and the effectors AexT and AexU in the Aeromonas veronii group. DNA Cell Biol. 28:383-388.

Swithers KS, Gogarten JP, Fournier GP (2009) Trees in the Web of Life, Journal of Biology 2009, 8:54 doi:10.1186/jbiol160

Fournier GP, Huang JL, Gogarten JP (2009) Horizontal gene transfer from extinct and extant lineages: Biological innovation and the coral of life. Philos Trans R Soc Lond B Biol Sci. 364 (1527):2229-39.

Kanisicak, O., Mendez, J. J., Yamamoto, S., Yamamoto, M., and Goldhamer, D. J. (2009). Progenitors of skeletal muscle satellite cells express the muscle determination gene, MyoD. Dev. Biol. 332, 131 141.

R.T. Emeny, G. Marusov, D.A. Lawrence, J. Pederson-Lane, X. Yin, M.A. Lynes, Manipulations of metallothionein gene dose accelerate the response to Listeria monocytogenes, Chemico-Biological Interactions (2009), doi:10.1016/j.cbi.2009.06.018

Marcus P.I., Ngunjiri J.M. and M.J. Sekellick. 2009. Dynamics of Biologically Active Subpopulations of Influenza Virus: Plaque-Forming, Noninfectious Cell-Killing, and Defective-Interfering Particles. J. Virol. doi:10.1128/JVI.02680-08

Guardino, K.M., Sheftic, S.R., Slattery, R.E., & Alexandrescu, A.T. (2009) “Hallmarks of conserved and non-conserved structures in the OB-fold superfamily”. Int. J. Mol. Sci. 10, 2412-2430

Patil, S.M., Xu, S., Sheftic, S.R., & Alexandrescu, A.T. (2009) “Dynamic alpha-helix structure of micelle-bound human amylin”, J Biol Chem, 284, 11982-11991

Heinicke, L.A., Wong, C.J., Lary, J., Nallagatla, S.R., Deigelman-Parente, A., Zheng, X., Cole, J.L. and Bevilacqua, P.C. (2009) RNA Dimerization promotes PKR dimerization and activation. J. Mol. Biol. doi:10.1016/j.jmb.2009.05.005

Whitaker, I. S., C. Kamya, E. A. Azzopardi, J. Graf, M. Kon, W. C. Lineaweaver. 2009. Preventing infective complications following leech therapy: is practice keeping pace with current research? Microsurgery in press.

Papke RT (2009) A critique of prokaryotic species concepts. Methods Mol Biol 532:379-95.

Noll KM, Thirangoon K (2009) Interdomain transfers of sugar transporters overcome barriers to gene expression. Methods Mol Biol 532:309-22.

Huang J, Gogarten JP (2009) Ancient gene transfer as a tool in phylogenetic reconstruction. Methods Mol Biol. 2009; 532:127-39.

Olendzenski L, Gogarten JP (2009) Gene transfer: who benefits? Methods Mol Biol. 2009;532:3-9.

Poptsova M (Gogarten Lab)(2009) Testing phylogenetic methods to identify horizontal gene transfer. Methods Mol Biol. 2009;532:227-40.

Fournier G (Gogarten Lab) (2009) Horizontal gene transfer and the evolution of methanogenic pathways. Methods Mol Biol. 2009;532:163-79.

Gogarten, M.B., Gogarten, J.P., Olendzenski, L.C. (editors), (2009) Horizontal Gene Transfer: Genomes in Flux. Humana Press - Springer ISBN-13: 978-1603278522

Alexandrescu, A. T. & Croke, R.L. (2008) “NMR of Amyloidogenic proteins”, in Protein Misfolding ISBN 978-1-60456-881-3

Croke, R.L., Sallum, C.O., Watson, E., Watt, E.D. & Alexandrescu, A. T. (2008) “Hydrogen exchange of monomeric a-synuclein shows unfolded structure persists at physiological temperature and is independent of molecular crowding in Escherichia coli”. Protein Science 17, 1434-1445.

Lounev, V. Y., Ramachandran, R., Wosczyna, M. N., Yamamoto, M., Maidment, A. D. A., Shore, E. M., Glaser, D. L., Goldhamer, D. J., and Kaplan, F. S. (2009). Identification of progenitor cells that contribute to heterotopic skeletogenesis. J Bone Joint Surg 91:652-663.

Mellone, B.G. (2009). Structural and temporal regulation of centromeric chromatin. Biochem Cell Biol. 87(1):255-64.

Yamamoto, M., Shook, N. A., Kanisicak, O., Yamamoto, S., Wosczyna, M. N., Camp, J. R., and Goldhamer, D. J. (2009). A multifunctional reporter mouse line for Cre- and FLP-dependent lineage analysis. Genesis 47, 107-114.

VanOudenhove, J., Anderson, E., Krueger, S. and Cole, J.L. (2009) Analysis of PKR structure by small angle scattering. J. Mol. Biol. doi:10.1016/j.jmb.2009.02.019

Lapierre P, Gogarten JP (2009) Estimating the size of the bacterial pan-genome Trends in Genetics, doi:10.1016/j.tig.2008.12.004

Carone DM, Longo MS, Ferreri GC, Hall L, Harris M, Shook N, Bulazel KV, Carone BR, Obergfell C, O'Neill MJ, O'Neill RJ. 2008. A new class of retroviral and satellite encoded small RNAs emanates from mammalian centromeres. Chromosoma. 2008 Oct 7. [Epub ahead of print]

Erhardt, S., Mellone B. G., Betts, C. M. et al. 2008. Genome-wide analysis reveals a cell cycle-dependent mechanism controlling centromere propagation. The Journal of Cell Biology. Vol. 183 No. 5: 805-818

Nyholm, S. V. et al. 2008. Recognition between symbiotic Vibrio fischeri and the haemocytes of Euprymna scolopes. Environ. Microbiol. 9:1462-2920.

Nukaga, M., C. R. Bethel, J. M. Thomson, A. M. Hujer, A. Distler, V. E. Anderson, J. R. Knox and R. A. Bonomo. 2008. Inhibition of class A ß-lactamases by carbapenems: Crystallographic observation of two conformations of meropenem in SHV-1. J. Am. Chem. Soc. 130: 12656–12662.

Laufer, A., M. Siddall and J. Graf. 2008. Characterization of the Digestive-Tract Microbiota of Hirudo orientalis, a European Medicinal Leech. Appl. Environ. Microbiol. 74:6151-6154.

Edrington TC, Bennett MP, Albert AD. 2008. Calorimetric Studies of Bovine Rod Outer Segment Disk Membranes Support a Monomeric Unit for Both Rhodopsin and Opsin. Biophys J. Jun 27. Epub ahead of print.

deLivron, M.A. and Robinson, V.L. (2008) Salmonella enterica sv. Typhimurium BipA Exhibits Two Distinct Ribosome Binding Modes J. Bacteriol. E-Publ. ahead of print.

Jinling Huang and J. Peter Gogarten (2008) Concerted gene recruitment in early plant evolution Genome Biology 9(7): R109

Lemaire, P.A., Anderson, E., Lary, J. and Cole, J.L. (2008) Mechanism of PKR activation by dsRNA. J. Mol. Biol. 381, 351-360.

Hou JM, D'Lima NG, Rigel NW, Gibbons HS, McCann JR, Braunstein M, Teschke CM. (2008) ATPase activity of Mycobacterium tuberculosis SecA1 and SecA2 proteins and its importance for SecA2 function in macrophages. J Bacteriol. 190:4880-7.

Hamel, L., Nahar, N., Poptsova, M.S., Zhaxybayeva, O. and Gogarten, J.P. 2008. Unsupervised Learning in Detection of Gene Transfer.Journal of Biomedicine and Biotechnology [Epub ahead of print] doi: 10.1155/2008/472719.

Santos CL, Vieira J, Tavares F, Benson DR, Tisa LS, Berry AM, Moradas-Ferreira P, Normand P. 2008. On the nature of fur evolution: a phylogenetic approach in Actinobacteria. BMC Evol Biol. 25:8:185. [Epub ahead of print];PMID: 18578876.

Sudi J, Zhang S, Intrieri G, Hao X, Zhang P. Coincidence of p-insertion sites and breakpoints of deletions induced by activating p elements in Drosophila. Genetics. 2008. 179:227-35.

Eric Anderson and James L. Cole 2008. Domain stabilities in PKR: evidence for weak interdomain interactions. Biochemistry 47: 4887-4897.

Arango-Pinedo, C., Bringhurst, R.M. and D. J. Gage (2008). Sinorhizobium meliloti mutants lacking phosphotransferase system enzyme HPr or EIIA are altered in diverse processes, including carbon metabolism, cobalt requirements, and succinoglycan production. J. Bacteriol. 190:2947

Noll KM, Lapierre P, Gogarten JP and Nanavati DM (2008) Evolution of mal ABC transporter operons in the Thermococcales and Thermotogales
BMC Evolutionary Biology 2008, 8:7

Metcalfe, C.J., K.V. Bulazel, G. C. Ferreri, W. Rens, E. Schroeder-Reiter, G. Wanner, M. D. B. Eldridge, and R. J. O'Neill. 2007. Genomic instability within centromeres of interspecific marsupial hybrids. Genetics 177: 2507-2517.

Brown, J.D., D. Golden, R.J.O’Neill. 2008. Methylation perturbations in retroelements within the genome of a Mus interspecific hybrid correlate with double minute chromosome formation. Genomics 91: 267-273.

Sen, A., S. Sur, A. K. Bothra, D. R. Benson, P. Normand and L. S. Tisa. 2008. The implication of life style on codon usage patterns and predicted highly expressed genes for three Frankia genomes. Antonie van Leeuwenhoek Published on-line, Feb.

Robertson, P.D., Warren, E.M., Zhang, H., Friedman, D.B., Lary, J.W., Cole, J.L., Tutter, A.V., Walter, J.C., Fanning, E., Eichman, B.F. (2008) Domain architecture and biochemical characterization of vertebrate MCM10. J. Biol. Chem. 83, 3338-3348.

Fournier, Gregory P., and Gogarten, J. Peter (2008) Evolution of Acetoclastic Methanogenesis in Methanosarcina via Horizontal Gene Transfer from Cellulolytic Clostridia J. Bacteriol. 190(3): 1124-7 [Abstract] [online] [PDF]

Sharma, AK, Zhaxybayeva, O., Papke, RT, Doolittle, WF. 2008. Actinorhodopsins: proteorhodopsin-like gene sequence found predominantly in non-marine environments. Environmental Microbiology (OnlineEarly Articles). doi:10.1111/j.1462-2920.2007.01525.x

Juliana E Mastronunzio , L S Tisa , P. Normand and D R Benson. 2008. Comparative secretome analysis suggests low plant cell wall degrading capacity in Frankia symbiont. BMC Genomics 2008, 9:47

Ngunjiri, J. M., M. J. Sekellick and P. I. Marcus. 2008. Clonogenic Assay of Type A Influenza Viruses Reveals Noninfectious Cell-Killing (Apoptosis-Inducing) Particles. J. Virol. 0: JVI.02221-07 [published online ahead of print]

Spurling CC, Godman CA, Noonan EJ, Rasmussen TP, Rosenberg DW, Giardina C. 2007. HDAC3 overexpression and colon cancer cell proliferation and differentiation. Mol Carcinogenesis [EPub ahead of print, September].

J Peter Gogarten, Gregory Fournier and Olga Zhaxybayeva (2007) Gene transfer and the reconstruction of life's early history from the molecular record. Space Science Reviews [Epub ahead of print] DOI: 10.1007 /s11214-007-9253-8

Hadjout, N., X. Yin, D. A. Knecht, and M. A. Lynes. 2007. Automated real-time measurements of leukocyte chemotaxis. J Immunol Methods. 2007 320:70-80

Sun, C., S. L. Rusch, J. Kim and D. A. Kendall. 2007. Chloroplast SecA and Escherichia coli SecA have distinct lipid and signal peptide preferences. J. Bacteriol. 189:1171-1175.

M. Willian, Dagan, T., Koonin, E. B., Dipippo, J. L., Gogarten, J. P. and Lake, J. A. 2007. The Evolution of Eukaryotes, Letter on "Genomics and the irreducible nature of eukaryotic cells" Science 316:542-543

Huang, Jinling and J. Peter Gogarten (2007) Did an ancient chlamydial endosymbiosis facilitate the establishment of primary plastids? Genome Biology 8(6): R99

Laufer, H., Demir, N., Capulong, C, Pan, X., Biggers, W.J. 2006. Hormonal Responses to Lobsters of Long Island Sound. Long Island Sound Research Conference Proceedings. 7:41-43.

Zhaxybayeva O, Gogarten JP, Doolittle WF (2007) A hyperconserved protein in Prochlorococcus and marine Synechococcus. FEMS Microbiol Lett. 274 (1): 30-4.

Silver, A.C., N. M. Rabinowitz, S. Küffer and J. Graf. 2007. Identification of Aeromonas veronii genes required for colonization of the medicinal leech, Hirudo verbana. J Bacteriol. 189:6763-72.

Fournier, G. P. and J. P. Gogarten. 2007. Signature of a primitive genetic code in ancient protein lineages. J. Mol. Evol. 65:425-36.

R.T. Papke, O. Zhaxybayeva, E. Feil, K. Sommerfeld, D. Muise and W.F. Doolittle. 2007. Searching for species in haloarchaea. PNAS 104:14092-14097.

Q. Yan., V.N. Malashkevich, A. Fedorov, E. Fedorov, E. Cao, J.W. Lary, J.L. Cole, S.G. Nathenson and S.C. Almo. 2007. Structure of CD84 provides insight into SLAM family function. PNAS 104: 10583-10588.

E. Watson, W.M. Matousek, E.L. Irimies, A.T. Alexandrescu 2007. Partially folded states of staphylococcal nuclease highlight the conserved structural hierarchy of OB-fold proteins. Biochemistry 46:9484-9494.

Huang, Jinling and J. Peter Gogarten (2007) Did an ancient chlamydial endosymbiosis facilitate the establishment of primary plastids? Genome Biology 8(6): R99

M. A. Lynes, J. Kang, S. L. Sensi, G. A. Perdrizet, and L. E. Hightower. 2007. Heavy metal ions in normal physiology, toxic stress and cytoprotection. Ann N Y Acad Sci. May 4 e-pub

A. C. Silver, Y. Kikuchi, A. A. Fadl, J. Sha, A. K. Chopra, and J. Graf. 2007. Interaction between innate immune cells and a bacterial type III secretion system in mutualistic and pathogenic associations. PNAS 104:9481-9486.

Normand, P., P. Lapierre, L. S. Tisa, J. P. Gogarten, N. Alloisio, E.Bagnarol, C.A. Bassi, A.M. Berry, D. M. Bickhart, N. Choisne,, A. Couloux, B. Cournoyer, S. Cruveiller, V. Daubin, N. Demange, M. P. Francino, E. Goltsman, Y. Huang, O.R. Kopp, L. Labarre, A. Lapidus, C. Lavire, J. Marechal, M. Martinez, J. E. Mastronunzio, B. C. Mullin, J. Niemann, P. Pujic, T. Rawnsley, Z. Rouy, C. Schenowitz, A. Sellstedt, F. Tavares, J. P. Tomkins, D.Vallenet, C. Valverde, L.G. Wall, Y.Wang, C. Medigue, & D. R. Benson. 2007. Genome sizes of facultatively symbiotic Frankia sp. strains reflect host plant biogeography. Genome Res. 17:7-15